PROFASI
Version 1.5
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Radius of gyration of a section of a protein chain. More...
#include <Rg.hh>
Public Member Functions | |
int | init_obs () |
All observables must implement one initialize routine. | |
void | of_chain (int i) |
Limit to chain i. If i is -1, all chains. | |
double | evaluate () |
Actual calculation of the value of the observable. | |
void | rangeEstimate (double &x1, double &x2) |
Estimate a range in which values of this observable are expected. | |
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void | set (std::string cmd) |
Give the object an instruction to process during initialization. | |
virtual void | refresh () |
Necessary before an observable value is used. | |
virtual double | delta (Update *u) |
Quick estimate of the change in an Observable due to an update. | |
double | operator() () |
Retrieve the value of the observable. | |
double | Value () |
Retrieve the value of the observable. | |
void | disable_stats () |
Stop collecting statistical data like averages and histograms. | |
void | enable_stats () |
Start collecting statistical data like averages and histograms. | |
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Named () | |
Create an object with name "unnamed". | |
Named (const char *st) | |
Create an object with name st given as a C string. | |
Named (std::string st) | |
Create an object with a name given as a string. | |
std::string | Name () const |
Retrive the name of an object. | |
void | Name (std::string gnm) |
Assign a new name to an object. | |
This observable returns the radius of gyration of all non-hydrogen atoms of a given chain or of the whole population. In the case of rg over many chains, it is assumed that EnforceBC has been called, so that all coordinates are within one unit periodic box. Only non-hydrogen atoms are used in the calculation.
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Even if it seems that one particular observable might need additional arguments during initialization, it is advantageous to have a uniform syntax for all of them. So, when additional arguments are needed, one should provide them in a separate function called before initialization, and then call init_obs without arguments. The name init_obs instead of a more natural "init" or "initialize" is because an Observable often inherits from other classes which represent its character more fundamentally. So, the names such as "init" are kept free for such base classes.
Reimplemented from prf::Observable.
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virtual |
The default is between 0 and 1. So, for observables with values always between 0 and 1, you need not over-write this virtual function. Sometimes the observable will have a different fixed range, determined by its definition. Sometimes the range can not be determined perfectly. In such a case, let this function just return something reasonable.
Reimplemented from prf::Observable.